Genetic diversity of arabica coffee varieties from the Royal Project Foundation using genotyping-by-sequencing (GBS)
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Abstract
Arabica coffee is one of the essential crops in the highland areas in Northern Thailand. Agro-morphological characterization, leaf rust resistance, and selected elite lines of these crops have been studied. However, little is known about the genetic diversity of Arabica coffee conserved by the Royal Project Foundation. This research used the genotyping-by-sequencing (GBS) method to investigate the genetic diversity of 23 Arabica coffee varieties. The results revealed that sequencing generated 1,945,389 average high-quality read tags per sample, of which 95.83% were successfully aligned to the reference genome. The total number of SNPs and InDels detected in the whole genome were 1,180,245 and 115,112 positions, respectively. The SNP dataset was used to analyze the pairwise similarity among populations based on the p-distance method, revealing narrow genetic diversity values from 0.14 to 0.56. The phylogenetic tree was divided into three main groups with a common ancestor. Moreover, the selected polymorphism of SNPs and InDels were developed to be molecular markers for coffee plant genetics studies. The outcome can evolve molecular markers and applications for plant breeding.
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